As others have pointed out before, the whole persistent-ball-o'-lightning-after-appearing thing is reminiscent of the old FFE/FE2 "hyperspace remnants". On the basis of this video evidence I strongly suspect that Capital Ships still have old-style hyperdrives installed rather than Frame Shift Drives, either because the FSD simply doesn't work for things that big or because retrofitting them into the Fleet would be too expensive and time-consuming. I don't think we've ever been told how many capital ships each side has, but since they never seem to actually be destroyed and there's hundreds of warzones where they can appear at any given moment in the game, I suspect the answer is (or ought to be ) "thousands of them".